Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion

Llarena, Ann-Katrin; Zhang, Ji; Vehkala, Minna; Välimäki, Niko; Hakkinen, Marjaana; Hänninen, Marja Liisa; Roasto, Mati; Mäesaar, Mihkel; Taboada, Eduardo N.; Barker, Dillon; Garofolo, Giuliano; Cammà, Cesare; Giannatale, Elisabetta Di; Corander, Jukka; Rossi, Mirko

doi:10.1099/mgen.0.000088

Cited by 26 publications

(29 citation statements)

References 67 publications

(94 reference statements)

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“…In contrast to raccoon-adapted clades, 78% of isolates in clade B, which contained approximately 30% of raccoon isolates in this study, were from subtypes with mixed-host association. Mixed-source genotypes have been well-described and typically include representatives from Clonal Complexes (CCs) described as 'generalists' including ST-45, ST-21, and ST-48 (52)(53)(54)(55). These CCs are highly prevalent worldwide, known for their broad host distribution, including livestock, and high burden of human illness.…”

Section: Discussionmentioning

confidence: 99%

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover

et al. 2020

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Free-ranging wildlife are increasingly recognized as potential reservoirs of disease-causing Campylobacter species such as C. jejuni and C. coli. Raccoons (Procyon lotor), which live at the interface of rural, urban, and more natural environments, are ideal subjects for exploring the potential role that wildlife play in the epidemiology of campylobacteriosis. We studied the prevalence and genetic diversity of Campylobacter from live-captured raccoons on five swine farms and five conservation areas in southwest Ontario. From 2011 to 2013, we collected fecal swabs (n = 1,096) from raccoons, and (n = 50) manure pit samples from the swine farm environment. We subtyped the resulting Campylobacter isolates (n = 581) using Comparative Genomic Fingerprinting (CGF) and 114 distinct subtypes were observed, including 96 and 18 subtypes among raccoon and manure pit isolates, respectively. Campylobacter prevalence in raccoons was 46.3%, with 98.7% of isolates recovered identified as C. jejuni. Novel raccoon-specific CGF subtypes (n = 40/96) accounted for 24.6% (n = 143/581) of Campylobacter isolates collected in this study. Our results also show that C. jejuni is readily acquired and lost in this wild raccoon population and that a high Campylobacter prevalence is observed despite transient carriage typically lasting 30 days or fewer. Moreover, although raccoons appeared to be colonized by species-adapted subtypes, they also harbored agriculture-associated genotypes that accounted for the majority of isolates observed (66.4%) and that are strongly associated with human infections. This suggests that raccoons may act as vectors in the transmission of clinically-relevant C. jejuni subtypes at the interface of rural, urban, and more natural environments.

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Section: Discussionmentioning

confidence: 99%

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover

et al. 2020

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“…In a follow-up publication, Llarena et al investigated the nature of the population structure of ST-45 clonal complex (CC), focusing on identifying a possible spatial-temporal evolutionary signal. The authors found that the occurrence and strength of the geographical signal varied between sublineages of ST-45 CC strains, but they could not find evidence of a temporal signal (6). In addition, the authors unexpectedly identified certain sublineages of ST-45 with extremely similar genomes regardless of the time and location of sampling.…”

Section: Defining the Baseline Genomic Diversity Of C Jejunimentioning

confidence: 94%

“…In addition, the authors unexpectedly identified certain sublineages of ST-45 with extremely similar genomes regardless of the time and location of sampling. These successful monomorphic clones were persistently isolated from animal hosts and human patients over a decade, from several countries around the world (6). There is no reason to think that clonal dispersal is limited to certain sublineages of ST-45.…”

Section: Defining the Baseline Genomic Diversity Of C Jejunimentioning

confidence: 99%

Whole-Genome Sequencing in Epidemiology of Campylobacter jejuni Infections

2017

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This review describes the current state of knowledge regarding the application of whole-genome sequencing (WGS) in the epidemiology of Campylobacter jejuni, the leading cause of bacterial gastroenteritis worldwide. We describe how WGS has increased our understanding of the evolutionary and epidemiological dynamics of this pathogen and how WGS has the potential to improve surveillance and outbreak detection. We have identified hurdles to the full implementation of WGS in public health settings. Despite these challenges, we think that ample evidence is available to support the benefits of integrating WGS into the routine monitoring of C. jejuni infections and outbreak investigations.KEYWORDS foodborne pathogens, genome analysis, molecular subtyping, surveillance studies T he ability to conduct epidemiological investigations and to intervene to control and to prevent foodborne and environmentally transmitted diseases is a major task of public health authorities. The identification, over a short period of time, of a sudden increase in the number of expected cases of a disease in a population in a limited geographical area (point-source outbreak) or clusters of cases with a presumptive common source not necessarily clustered geographically (diffuse outbreak) depends on knowledge of the baseline infectious state of the population regarding that disease, which is usually acquired through surveillance. In this regard, identifying epidemiologically linked cases and differentiating them from concurrent sporadic incidences are essential for risk assessment, outbreak investigations, and source attribution for foodborne pathogens. These processes have relied increasingly on traditional epidemiological investigations supplemented with molecular subtyping of the etiological agent, and no method offers a higher degree of resolution than whole-genome sequencing (WGS). The recent development of high-throughput sequencing technologies for WGS (i.e., next-generation sequencing [NGS]) has resulted in large-scale sequencing of various pathogens. Allowing the detection of all possible epidemiologically significant variations between strains (1), WGS is progressively replacing traditional typing methods (serotyping, phenotyping, pulsed-field gel electrophoresis [PFGE], and amplified fragment length polymorphism [AFLP] analysis) and sequence-based investigations (PCR-based methods). Moreover, the declining costs of NGS and the availability of benchtop analyzers are increasingly facilitating the application of WGS for routine surveillance and outbreak investigations of bacterial and viral infectious diseases by public health authorities (2). As a result, WGS analysis is currently being used in several countries for real-time surveillance of Listeria monocytogenes and Salmonella enterica (http://www.fda.gov/Food/FoodScience Research/WholeGenomeSequencingProgramWGS) (3), and similar approaches for other foodborne pathogens are expected to come into use shortly. Campylobacter jejuni is one of the most frequent causes of bacterial g...

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“…Multilocus sequence typing (MLST) has been an invaluable molecular typing method, providing essential knowledge about C. jejuni types occurring in various hosts and sources worldwide. MLST is, however, limited to the characterization and discrimination of isolates according to sequence type (ST) (11)(12)(13); thus, more accurate methods, such as whole-genome MLST (wgMLST), are increasingly being used (11,14) to compare genetically related isolates in more detail and to be able to identify clones potentially originating from the same source. In previous studies, most of the STs found among wild birds, including mallard ducks (5), barnacle geese (7), starlings (15), and several other bird species (16), have been considered to represent mainly hostassociated STs, differing from those STs reported in human patients or domestic animals.…”

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confidence: 99%

Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland

Kovanen

Rossi

Pohja-Mykrä

et al. 2019

Appl Environ Microbiol

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Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention. IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.

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Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion

Cited by 26 publications

References 67 publications

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover

Campylobacter jejuni Strain Dynamics in a Raccoon (Procyon lotor) Population in Southern Ontario, Canada: High Prevalence and Rapid Subtype Turnover

Whole-Genome Sequencing in Epidemiology of Campylobacter jejuni Infections

Population Genetics and Characterization of Campylobacter jejuni Isolates from Western Jackdaws and Game Birds in Finland

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